Owain.. Engine and chaincase are completely separate, so there is no mixing of the oils. All engines produce varying quantities of metallic debris, and without knowing its previous history it is difficult to tell whether this material is "old stuff" being washed out or a new problem. In the absence of any major catastrophic impending doom noises I would be inclined to wash out the tank and sump as best you can, remove muck and sediment from nooks and crannies in the timing case, refill with fresh oil and remove the sump plate from time to time to see if the situation continues. That way you can plan for remedial work, and get a firm idea whether a problem exists. As it has been recently bored, I would expect some nice new shiny bits in the oil.
Clutch Chainwheel...They all rock a little bit, the design relies on a single row of rollers, so not much stability even when new. Remove the clutch for inspection, you should find the gearbox input shaft has no lateral movement. This is controlled by a ball race at the kickstart ratchet end of the mainshaft. A large circular flat thrust washer locates the clutch, this fits over two semi circular steel half rings (abutment ring in the parts book). The gearbox input shaft is splined, not tapered, so all this just pulls off. Loss or failure of this thrust arrangement will allow the chainwheel to contact the inner chaincase and allow the centre retaining nut to loosen. The groove in the mainshaft for the two half rings is shallow, so pay close attention to their correct fitment.
Damage and wear on the roller "tracks" means new parts, but short term a set of new rollers will offer a small improvement. Grease the rollers on assembly.
Give the big clutch retaining nut some Loctite, even though there is a tab washer, inner shaped to fit the input shaft splines. Give it a good tighten with the old "put in top gear, brake on" trick.
Make a nice tubular peg spanner for the cush drive crank nut, it needs to be well tight, 60-70 Ft/lbs is suggested. Most are butchered by hammer and drift.
Swarfy.
Additional. See you have the clutch off now, have a good look at the abutment rings as they have to support the whole clutch, a bit like hanging on with just fingertips. the groove is less than 1.5mm deep. Turn them over to put an undamaged inner edge towards the gearbox. Stick them to the shaft with a dab of grease, then carefully place the thrust washer over them. Originally this washer came in varying thicknesses to assist in chain alignment. When I first got my bike the half rings were missing, the thrust washer happily running on the three rivet heads that hold the oilseal carrier!
